Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007064.1 Hibiscus syriacus cultivar Beakdansim tig00018351_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 49947
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:11116 original size:18 final size:18
Alignment explanation
Indices: 11093--11165 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
11083 ACTGAATATT
11093 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
11111 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
11130 TTATTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
11149 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
11166 GTATATGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:11442 original size:24 final size:21
Alignment explanation
Indices: 11386--11443 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
11376 ATATATTCTC
11386 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
11408 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
11432 GATCACTTTCAT
1 -ATCACTTTCAT
11444 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:11957 original size:19 final size:19
Alignment explanation
Indices: 11929--11980 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
11919 TTTAAGTAGG
11929 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
* *
11948 TGCTTCGATGCACTCCTTA
1 TGCATCGATGCACTCCTCA
*
11967 TTCATCGATGCACT
1 TGCATCGATGCACT
11981 AATTGCATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:15473 original size:21 final size:21
Alignment explanation
Indices: 15447--15502 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
15437 CTTTGTCCAA
*
15447 TAATTCTTGTAATTGAATCTT
1 TAATTCTTGTAATTAAATCTT
15468 TAATTCTTGTAATTAAATCTT
1 TAATTCTTGTAATTAAATCTT
15489 TAATTCTTGTAATT
1 TAATTCTTGTAATT
15503 CTTTTGGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (21 bp):
TAATTCTTGTAATTAAATCTT
Found at i:18151 original size:20 final size:20
Alignment explanation
Indices: 18123--18160 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18113 CACTGAATAT
18123 TTGTCCCGAAGAACCACTGA
1 TTGTCCCGAAGAACCACTGA
*
18143 TTGTTCCGAAGAACCACT
1 TTGTCCCGAAGAACCACT
18161 ATATCCCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAGAACCACTGA
Found at i:18936 original size:19 final size:19
Alignment explanation
Indices: 18912--18955 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
18902 TTTAAGTAGG
*
18912 TGCATCGATGCAGTCCTCA
1 TGCATCGATGCACTCCTCA
*
18931 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTCA
18950 TGCATC
1 TGCATC
18956 AATGAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:21478 original size:24 final size:24
Alignment explanation
Indices: 21451--21532 Score: 57
Period size: 24 Copynumber: 3.6 Consensus size: 24
21441 AAAAAAACGT
21451 AAATGAACATAAATGAACGTAGAC
1 AAATGAACATAAATGAACGTAGAC
* * * *
21475 AAAT-AA-A-ACA--AACGAACAT
1 AAATGAACATAAATGAACGTAGAC
* * *
21494 AAATAAATATAAAAGAACGTAGAC
1 AAATGAACATAAATGAACGTAGAC
21518 AAATGAACATTAAAT
1 AAATGAACA-TAAAT
21533 TAATTGAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 11
0.65 0.17 0.17
Matches are distributed among these distances:
19 10 0.24
20 2 0.05
21 3 0.07
22 3 0.07
23 2 0.05
24 17 0.41
25 4 0.10
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (24 bp):
AAATGAACATAAATGAACGTAGAC
Found at i:24415 original size:17 final size:16
Alignment explanation
Indices: 24334--24415 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 16
24324 ATGACATTAT
*
24334 ATTAAAATAAAATAAAA
1 ATTAAAAT-TAATAAAA
*
24351 ATTAAAAATTATATATAA
1 ATT-AAAATTA-ATAAAA
* *
24369 TTTAAAA-AAATAAAA
1 ATTAAAATTAATAAAA
24384 ATTTAAATATT-ATAACAA
1 A-TTAAA-ATTAATAA-AA
24402 ATTAAAATTAATAA
1 ATTAAAATTAATAA
24416 TTTATATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
15 5 0.10
16 9 0.18
17 22 0.43
18 15 0.29
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAATTAATAAAA
Found at i:24415 original size:34 final size:34
Alignment explanation
Indices: 24334--24415 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
24324 ATGACATTAT
*
24334 ATTAAAATAAAATAAAAATTAAAAATTATATATAA
1 ATTAAAAT-AAATAAAAATTAAAAATTATATACAA
* *
24369 TTTAAAA-AAATAAAAATTTAAATATTATA-ACAA
1 ATTAAAATAAATAAAAA-TTAAAAATTATATACAA
*
24402 ATTAAAATTAATAA
1 ATTAAAATAAATAA
24416 TTTATATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 18 0.45
34 16 0.40
35 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (34 bp):
ATTAAAATAAATAAAAATTAAAAATTATATACAA
Found at i:24420 original size:24 final size:24
Alignment explanation
Indices: 24345--24430 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 24
24335 TTAAAATAAA
*
24345 ATAAAAATTAAAAATTATATATAATTT
1 ATAAAAAATAAAAA-T-TA-ATAATTT
*
24372 A-AAAAAATAAAAATTTA-AATATT
1 ATAAAAAATAAAAATTAATAAT-TT
* *
24395 ATAACAAATTAAAATTAATAATTT
1 ATAAAAAATAAAAATTAATAATTT
24419 ATATAATAAATA
1 ATA-AA-AAATA
24431 CGTAATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
22 3 0.06
23 4 0.09
24 19 0.40
25 5 0.11
26 15 0.32
27 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAAAAATAAAAATTAATAATTT
Found at i:40889 original size:21 final size:21
Alignment explanation
Indices: 40857--40899 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
40847 TGTTTGTTTA
40857 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
40878 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
40899 A
1 A
40900 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:42054 original size:15 final size:16
Alignment explanation
Indices: 42021--42056 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
42011 CGTAAAAAGT
*
42021 AATAAAATATTAGTAA
1 AATAAAATATTAATAA
42037 AATAAAAT-TTAATAA
1 AATAAAATATTAATAA
42052 AATAA
1 AATAA
42057 TAGATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAAAATATTAATAA
Found at i:46588 original size:10 final size:10
Alignment explanation
Indices: 46573--46597 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46563 CACCTGTCAC
46573 CGCGGTGTTA
1 CGCGGTGTTA
46583 CGCGGTGTTA
1 CGCGGTGTTA
46593 CGCGG
1 CGCGG
46598 AGGAAGGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.24, G:0.44, T:0.24
Consensus pattern (10 bp):
CGCGGTGTTA
Done.